so, modal dialogs:
i think they just need to add the dialog box itself.
so you get 10 messages all at once, the dialog would say:
"message"
[close] [action]
10 others [close all]
providing you an option to quickly clear the deck that would work in all apps.
then you would have a "notification app", which might not actually be an "app", but a "page" to the left of spotlight or some other UI gimmick. this "app" would list all your notifications in sequence, with some kind of tab to view to view only "unread notifications" that had been missed by tapping "close all".

or maybe apple just forces people to tap "close" ten times, and then unsubscribe from some services.
the problem might not be the UI, but that people are oversubscribed to too many alerts. so many that UI improvements would only help people ignore them to the point that they become less and less useful.

i kinda pictured to work like this:
you get the normal pop-up msg box that you're used to, but they give you 3 options: close, view, minimize
minimize would drop the little numbering bubble onto the each app. adding to it (similar to how it works in mail, app store updates, etc.) if you choose minimize, then all updates are automatically added to the stack and it assumes you dont want that app to bother you again until you open it to see the notifications.
"close" just means that you read the notification and dismissed it
"view" opens the app to see the notification.
i dont think an app would be necessary to view all notifications and you wouldn't need to pull a tab from the top. to see notifications all you would need to do is do a downward swipe from ANY of your pages (as long as you're not in an app) since that gesture currently does nothing from any of the "home screen pages". this would bring you to notification pages which would have each and every app that has notification bubbles on them. and since they are a separate stack from your normal app pages, you could swipe sideways to have pages of notifications (if you had that many apps). to leave the notification pages, just swipe upward to bring you back to your normal application pages.